I got greedy and wanted to get the last upgrade to Nook's store today, so I went ahead and placed Memory Card B into Slot 2.
Started a town, got through the tutorial, etc. All done on Slot 2's Memory Card.
To do this, I removed the memory card from Slot A.
After I was done, I put the memory card back into slot A.
When I tried opening the game in slot A again, it told me that my memory card was corrupted/needed to be formatted, and that if I chose to format it, my save would be lost.
I'm so distraught. I've been playing every day since Jan. 27th, almost had the perfect town, and had most furniture at this point. Is there ANY way I can restore my game???